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- PDB-8vwn: Crystal structure of Vibrio cholerae NFeoB in the GDP-bound form -

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Basic information

Entry
Database: PDB / ID: 8vwn
TitleCrystal structure of Vibrio cholerae NFeoB in the GDP-bound form
ComponentsFerrous iron transport protein B
KeywordsTRANSPORT PROTEIN / iron / transport / Feo / G-protein
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / : / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition / GTP binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ferrous iron transport protein B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.25 Å
AuthorsLee, M. / Smith, A.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133497 United States
National Science Foundation (NSF, United States)CHE1844624 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural determinants of Vibrio cholerae FeoB nucleotide promiscuity.
Authors: Lee, M. / Magante, K. / Gomez-Garzon, C. / Payne, S.M. / Smith, A.T.
History
DepositionFeb 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferrous iron transport protein B
B: Ferrous iron transport protein B
C: Ferrous iron transport protein B
D: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,45311
Polymers128,6074
Non-polymers1,8467
Water34219
1
A: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6193
Polymers32,1521
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6193
Polymers32,1521
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5952
Polymers32,1521
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6193
Polymers32,1521
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.270, 155.309, 50.916
Angle α, β, γ (deg.)90.000, 95.880, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 24 or resid 40 through 62 or resid 64 or resid 70 through 258))
d_2ens_1(chain "B" and (resid 2 through 24 or resid 40...
d_3ens_1(chain "C" and (resid 2 through 24 or resid 40 through 62 or resid 64 or resid 70 through 258))
d_4ens_1(chain "D" and (resid 2 through 68 or resid 70 through 258))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSGLYGLYAA2 - 242 - 24
d_12LYSLYSLEULEUAA40 - 6240 - 62
d_13SERSERSERSERAA6464
d_14SERSERARGARGAA70 - 25870 - 258
d_21LYSLYSGLYGLYBB2 - 242 - 24
d_22LYSLYSLEULEUBB40 - 6240 - 62
d_23SERSERSERSERBB6464
d_24SERSERSERSERBB6868
d_25ILEILEARGARGBB71 - 25871 - 258
d_31LYSLYSGLYGLYCC2 - 242 - 24
d_32LYSLYSLEULEUCC40 - 6240 - 62
d_33SERSERSERSERCC6464
d_34SERSERARGARGCC70 - 25870 - 258
d_41LYSLYSSERSERDD2 - 682 - 68
d_42SERSERARGARGDD70 - 25870 - 258

NCS oper:
IDCodeMatrixVector
1given(0.19730843489, 0.631295671257, -0.750023437616), (-0.900758850519, 0.418693469277, 0.115452466398), (0.386914557407, 0.65281050408, 0.651256916301)32.5022644681, 23.8186457813, -4.03041925531
2given(0.934575829331, 0.00149658786079, 0.355760845871), (-0.00542682146894, -0.999814833373, 0.0184620848355), (0.355722600967, -0.0191848688425, -0.934394655362)9.12360247383, -32.7863108026, -49.7492760267
3given(0.238706928436, -0.615953221312, -0.750746715925), (0.874055378147, 0.47314446392, -0.110279246436), (0.423138509532, -0.629869784493, 0.651320087464)30.2523863132, -64.5254381584, -15.8276571948

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Components

#1: Protein
Ferrous iron transport protein B


Mass: 32151.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: feoB_1, ERS013165_00117 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A655NVH2
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 3350, 0.2 M magnesium chloride, 0.1 M bis-tris pH 5.5, 0.1 M lithium chloride, 3 mM GDP

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12706 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12706 Å / Relative weight: 1
ReflectionResolution: 4.25→60.53 Å / Num. obs: 10461 / % possible obs: 98.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 139.16 Å2 / CC1/2: 0.983 / Net I/σ(I): 6.9
Reflection shellResolution: 4.25→4.33 Å / Num. unique obs: 447 / CC1/2: 0.356

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.25→50.65 Å / SU ML: 0.5978 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.9462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2694 515 4.95 %
Rwork0.2209 9881 -
obs0.2235 10396 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 150.83 Å2
Refinement stepCycle: LAST / Resolution: 4.25→50.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7754 0 133 1 7888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00347992
X-RAY DIFFRACTIONf_angle_d0.762710829
X-RAY DIFFRACTIONf_chiral_restr0.04551269
X-RAY DIFFRACTIONf_plane_restr0.00491369
X-RAY DIFFRACTIONf_dihedral_angle_d17.19913018
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.14776164342
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.980482345153
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.13303071406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.25-4.680.2871170.24872423X-RAY DIFFRACTION96.76
4.68-5.360.30551250.24982485X-RAY DIFFRACTION99.47
5.36-6.750.32561310.29872494X-RAY DIFFRACTION99.17
6.75-50.650.23361420.17312479X-RAY DIFFRACTION97.22

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